Best practices for the execution, analysis, and data storage of plant single-cell/nucleus transcriptomics.

DOI
Publisher DOI
PubMed ID
38231860
Abstract
Single-cell and single-nucleus RNA-sequencing (scRNA-seq and snRNA-seq) technologies capture the expression of plant genes at an unprecedented resolution. Therefore, these technologies are gaining traction in plant molecular and developmental biology for elucidating the transcriptional changes across cell types in a specific tissue or organ, upon treatments, in response to biotic and abiotic stresses, or between genotypes. Despite the rapidly accelerating use of these technologies, collective and standardized experimental and analytical procedures to support the acquisition of high-quality datasets are still missing. In this commentary, we discuss common challenges associated with the use of single-cell transcriptomics in plants and propose general guidelines to improve reproducibility, quality, comparability, and interpretation, and to make the data readily available to the community in this fast-developing field of research.
Date Issued
2024-03-29
Publication Type
Article
Subject(s)
Language(s)
en
Author(s)
Grones, Carolin
Eekhout, Thomas
Shi, Dongbo
Neumann, Manuel
Ke, Yuji
Shahan, Rachel
Cox, Kevin L
Gomez-Cano, Fabio
Nelissen, Hilde
Lohmann, Jan U
Giacomello, Stefania
Martin, Olivier C
Cole, Benjamin
Wang, Jia-Wei
Kaufmann, Kerstin
Palfalvi, Gergo
Greb, Thomas
Libault, Marc
De Rybel, Bert
Additional Credits
Journal
The Plant Cell
Publisher
American Society of Plant Biologists
ISSN
1040-4651
Access(Rights)
open.access
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